ArticleJournal of chemical theory and computation2021
Metadynamics-Based Approaches for Modeling the Hypoxia-Inducible Factor 2α Ligand Binding Process.
Article in Journal of chemical theory and computation, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed.
- Examining Genetic Variants Associated with FOXP1 Syndrome through Molecular Dynamics of Its DNA-Binding Domain and Self-Organizing Maps.Journal of chemical information and modeling · 2026Article
- Structural and Kinetic Basis for the Rational Design of Next-Generation β-Lactamase Inhibitors.Journal of medicinal chemistry · 2026Article
- Residence time in drug discovery: current insights and future perspectives.Pharmacological reports : PR · 2025Review
- Path-Based Nonequilibrium Binding Free Energy Estimation, from Protein-Ligand to RNA-Ligand Binding.Journal of chemical information and modeling · 2025Article
- SOMMD: an R package for the analysis of molecular dynamics simulations using self-organizing map.Bioinformatics (Oxford, England) · 2025Article
- Gating residues govern ligand unbinding kinetics from the buried cavity in HIF-2α PAS-B.Protein science : a publication of the Protein Society · 2024Article
- Exploring Product Release from Yeast Cytosine Deaminase with Metadynamics.The journal of physical chemistry. B · 2024Article
- Hypoxia modeling techniques: A review.Heliyon · 2023Review
- PathDetect-SOM: A Neural Network Approach for the Identification of Pathways in Ligand Binding Simulations.Journal of chemical theory and computation · 2022Article
- Weighted Ensemble Simulation: Advances in methods, software, and applications.Wiley interdisciplinary reviews. Computational molecular scienceArticle
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3 authors.
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Abstract
Several methods based on enhanced-sampling molecular dynamics have been proposed for studying ligand binding processes. Here, we developed a protocol that combines the advantages of steered molecular dynamics (SMD) and metadynamics. While SMD is proposed for investigating possible unbinding pathways of the ligand and identifying the preferred one, metadynamics, with the path collective variable (PCV) formalism, is suggested to explore the binding processes along the pathway defined on the basis of SMD, by using only two CVs. We applied our approach to the study of binding of two known ligands to the hypoxia-inducible factor 2α, where the buried binding cavity makes simulation of the process a challenging task. Our approach allowed identification of the preferred entrance pathway for each ligand, highlighted the features of the bound and intermediate states in the free-energy surface, and provided a binding affinity scale in agreement with experimental data. Therefore, it seems to be a suitable tool for elucidating ligand binding processes of similar complex systems.
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